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- PDB-6fsz: Structure of the nuclear RNA exosome -

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Entry
Database: PDB / ID: 6fsz
TitleStructure of the nuclear RNA exosome
Components
  • (Exosome complex component ...) x 9
  • (Exosome complex exonuclease ...) x 2
  • ATP-dependent RNA helicase DOB1
  • Exosome complex protein LRP1
  • M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog
  • RNA (5'-R(P*AP*AP*AP*AP*UP*UP*UP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsRNA / RNA exosome / Ribosome / pre-ribosome / Mtr4 / Helicase
Function / homologyDis3-like cold-shock domain 2 (CSD2) / Exoribonuclease, phosphorolytic domain 2 / Exosome complex component RRP45 / PIN-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / PNPase/RNase PH domain superfamily / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Exosome complex component, N-terminal domain / rRNA-processing arch domain / RNA-binding domain, S1 ...Dis3-like cold-shock domain 2 (CSD2) / Exoribonuclease, phosphorolytic domain 2 / Exosome complex component RRP45 / PIN-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / PNPase/RNase PH domain superfamily / Exosome complex RNA-binding protein 1/RRP40/RRP4 / Exosome complex component, N-terminal domain / rRNA-processing arch domain / RNA-binding domain, S1 / Ribonuclease II/R, conserved site / Ribosomal protein S5 domain 2-type fold / Exosome complex component CSL4, C-terminal / M-phase phosphoprotein 6 / ATP-dependent RNA helicase Ski2-like / Helicase superfamily 1/2, ATP-binding domain / Exosome complex exonuclease RRP44, S1 domain / ATP-dependent RNA helicase Ski2, C-terminal / Exosome-associated factor Rrp6, N-terminal / Nucleic acid-binding, OB-fold / Ribonuclease H-like superfamily / DEAD/DEAH box helicase domain / Prismane-like superfamily / Exosome-associated factor Rrp47/DNA strand repair C1D / HRDC-like superfamily / Sas10/Utp3/C1D / S1 domain / PIN domain / 3'-5' exonuclease domain / HRDC domain / Ribonuclease II/R / Exosome complex component Rrp43 / Rrp44-like cold shock domain / Exoribonuclease, phosphorolytic domain 1 / rRNA-processing arch domain / Exosome complex exonuclease Rrp40 N-terminal domain / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA decay by 3' to 5' exoribonuclease / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / HRDC domain profile. / S1 domain profile. / Ribonuclease II family signature. / Rrp44-like cold shock domain / S1 domain / KH domain / Exosome complex exonuclease RRP4 N-terminal region / PIN domain / Exosome component EXOSC1/CSL4 / Exoribonuclease, PH domain 2 superfamily / M-phase phosphoprotein 6 / DSHCT (NUC185) domain / PMC2NT (NUC016) domain / Sas10/Utp3/C1D family / 3' exoribonuclease family, domain 2 / 3'-5' exonuclease / 3' exoribonuclease family, domain 1 / RNB domain / HRDC domain / Helicase conserved C-terminal domain / DEAD/DEAH box helicase / Exosome complex component Csl4 / Rrp40, S1 domain / K Homology domain, type 1 superfamily / Helicase, C-terminal / K Homology domain, type 1 / regulation of exoribonuclease activity / ncRNA polyadenylation / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / ncRNA 3'-end processing / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / maturation of 5.8S rRNA / nuclear mRNA surveillance of mRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear polyadenylation-dependent CUT catabolic process / nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription / nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' / U1 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / nuclear retention of pre-mRNA at the site of transcription / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / CUT catabolic process / nuclear polyadenylation-dependent tRNA catabolic process / nuclear polyadenylation-dependent rRNA catabolic process / exosome (RNase complex) / nuclear exosome (RNase complex) / U4 snRNA 3'-end processing / polyadenylation-dependent snoRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone mRNA catabolic process / nuclear mRNA surveillance / nuclear-transcribed mRNA catabolic process, non-stop decay / Hydrolases, Acting on ester bonds, Endoribonucleases producing 5'-phosphomonoesters / rRNA metabolic process / posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery / ATP-dependent 3'-5' RNA helicase activity
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.6 Å resolution
AuthorsSchuller, J.M. / Falk, S. / Conti, E.
CitationJournal: Science / Year: 2018
Title: Structure of the nuclear exosome captured on a maturing preribosome.
Authors: Jan Michael Schuller / Sebastian Falk / Lisa Fromm / Ed Hurt / Elena Conti
Abstract: The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex ...The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60) during 7-to-5.8 rRNA processing. The cofactors of the nuclear exosome are sandwiched between the ribonuclease core complex (Exo-10) and the remodeled "foot" structure of the pre-60 particle, which harbors the 5.8 rRNA precursor. The exosome-associated helicase Mtr4 recognizes the preribosomal substrate by docking to specific sites on the 25 rRNA, captures the 3' extension of the 5.8 rRNA, and channels it toward Exo-10. The structure elucidates how the exosome forms a structural and functional unit together with its massive pre-60 substrate to process rRNA during ribosome maturation.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 20, 2018 / Release: Mar 21, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 21, 2018Structure modelrepositoryInitial release
1.1Apr 4, 2018Structure modelData collection / Database references / Source and taxonomy / Structure summaryentity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif_entity.details / _entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg
1.2Apr 25, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
2: RNA (5'-R(P*AP*AP*AP*AP*UP*UP*UP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
AA: Exosome complex component RRP45
BB: Exosome complex component SKI6
CC: Exosome complex component RRP43
DD: Exosome complex component RRP46
EE: Exosome complex component RRP42
FF: Exosome complex component MTR3
GG: Exosome complex component RRP40
HH: Exosome complex component RRP4
II: Exosome complex component CSL4
JJ: Exosome complex exonuclease DIS3
KK: Exosome complex exonuclease RRP6
LL: Exosome complex protein LRP1
MM: ATP-dependent RNA helicase DOB1
NN: M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog


Theoretical massNumber of molelcules
Total (without water)641,38915
Polyers641,38915
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 1 types, 1 molecules 2

#1: RNA chain RNA (5'-R(P*AP*AP*AP*AP*UP*UP*UP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 7158.137 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae (baker's yeast)

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Exosome complex component ... , 9 types, 9 molecules AABBCCDDEEFFGGHHII

#2: Protein/peptide Exosome complex component RRP45 / / Ribosomal RNA-processing protein 45


Mass: 33799.590 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP45, YDR280W, D9954.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05636
#3: Protein/peptide Exosome complex component SKI6 / / Extracellular mutant protein 20 / Ribosomal RNA-processing protein 41 / Superkiller protein 6


Mass: 27794.926 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SKI6, ECM20, RRP41, YGR195W, G7587 / Production host: Escherichia coli (E. coli) / References: UniProt: P46948
#4: Protein/peptide Exosome complex component RRP43 / / Ribosomal RNA-processing protein 43


Mass: 43977.805 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP43, YCR035C, YCR35C, YCR522 / Production host: Escherichia coli (E. coli) / References: UniProt: P25359
#5: Protein/peptide Exosome complex component RRP46 / / Ribosomal RNA-processing protein 46


Mass: 26913.988 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP46, YGR095C / Production host: Escherichia coli (E. coli) / References: UniProt: P53256
#6: Protein/peptide Exosome complex component RRP42 / / Ribosomal RNA-processing protein 42


Mass: 29294.398 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP42, YDL111C / Production host: Escherichia coli (E. coli) / References: UniProt: Q12277
#7: Protein/peptide Exosome complex component MTR3 / / mRNA transport regulator 3


Mass: 27559.869 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Strain: ATCC 204508 / S288c / Gene: MTR3, YGR158C, G6676 / Production host: Escherichia coli (E. coli) / References: UniProt: P48240
#8: Protein/peptide Exosome complex component RRP40 / / Ribosomal RNA-processing protein 40


Mass: 26778.551 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP40, YOL142W / Production host: Escherichia coli (E. coli) / References: UniProt: Q08285
#9: Protein/peptide Exosome complex component RRP4 / / Ribosomal RNA-processing protein 4


Mass: 39714.445 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP4, YHR069C / Production host: Escherichia coli (E. coli) / References: UniProt: P38792
#10: Protein/peptide Exosome complex component CSL4 / / CEP1 synthetic lethal protein 4


Mass: 32805.645 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CSL4, SKI4, YNL232W, N1154 / Production host: Escherichia coli (E. coli) / References: UniProt: P53859

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Exosome complex exonuclease ... , 2 types, 2 molecules JJKK

#11: Protein/peptide Exosome complex exonuclease DIS3 / Chromosome disjunction protein 3 / Ribosomal RNA-processing protein 44


Mass: 113983.898 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: DIS3, RRP44, YOL021C, O2197 / Production host: Escherichia coli (E. coli)
References: UniProt: Q08162, Hydrolases, Acting on ester bonds, Exoribonucleases producing 5'-phosphomonoesters, Hydrolases, Acting on ester bonds, Endoribonucleases producing 5'-phosphomonoesters
#12: Protein/peptide Exosome complex exonuclease RRP6 / Ribosomal RNA-processing protein 6


Mass: 84159.586 Da / Num. of mol.: 1 / Details: Inactive point mutant D296N / Mutation: D296N
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RRP6, UNC733, YOR001W / Production host: Escherichia coli (E. coli)
References: UniProt: Q12149, Hydrolases, Acting on ester bonds, Exoribonucleases producing 5'-phosphomonoesters

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Protein/peptide , 3 types, 3 molecules LLMMNN

#13: Protein/peptide Exosome complex protein LRP1 / / Like an rRNA processing protein 1 / Yeast C1D domain-containing protein / rRNA processing protein 47


Mass: 21086.297 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: LRP1, RRP47, YC1D, YHR081W / Production host: Escherichia coli (E. coli) / References: UniProt: P38801
#14: Protein/peptide ATP-dependent RNA helicase DOB1 / mRNA transport regulator MTR4


Mass: 122260.094 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MTR4, DOB1, YJL050W, J1158 / Production host: Escherichia coli (E. coli) / References: UniProt: P47047, RNA helicase
#15: Protein/peptide M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog,Nuclear exosome-associated RNA binding protein,M-phase phosphoprotein 6 homolog / Exosome-associated RNA-binding protein MPP6


Mass: 4101.711 Da / Num. of mol.: 1
Details: Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as ...Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MPP6, YNR024W, N3230 / Production host: Escherichia coli (E. coli) / References: UniProt: P53725

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Nuclear RNA exosomeCOMPLEX1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 150MULTIPLE SOURCES
2Nuclear RNA exosomeCOMPLEX2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 151RECOMBINANT
3nucleic acidCOMPLEX11NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
224932Saccharomyces cerevisiae (baker's yeast)
334932Saccharomyces cerevisiae (baker's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 38.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 22439 / Symmetry type: POINT

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